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- PDB-4fjk: RB69 DNA polymerase ternary complex with dATP/dA -

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Basic information

Entry
Database: PDB / ID: 4fjk
TitleRB69 DNA polymerase ternary complex with dATP/dA
Components
  • DNA polymerase
  • DNA primer
  • DNA template
KeywordsTransferase/DNA / dATP/dA / RB69 / RB69pol / quadruple / Transferase-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / : ...DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / : / Monooxygenase / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXia, S. / Wang, J. / Konigsberg, W.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase.
Authors: Xia, S. / Wang, J. / Konigsberg, W.H.
History
DepositionJun 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
T: DNA template
P: DNA primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0169
Polymers113,3253
Non-polymers6926
Water11,151619
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-74 kcal/mol
Surface area43000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.700, 120.202, 130.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase / Gp43


Mass: 104448.867 Da / Num. of mol.: 1 / Mutation: D222A, D327A, L415A, L561A, S565G, Y567A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA template


Mass: 4908.193 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA primer


Mass: 3967.585 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 625 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 150 mM CaCl2, 10% (w/v) PEG 350 monomethyl ether (MME), and 100 mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 15, 2011
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 79818 / Num. obs: 75753 / % possible obs: 94.9 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 1.1
Reflection shellResolution: 2→2.07 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.61 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.891 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22595 4006 5 %RANDOM
Rwork0.182 ---
all0.182 79818 --
obs0.18424 75753 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.013 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0 Å20 Å2
2--0.8 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7340 591 35 619 8585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198257
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.90811296
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4865912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35524.18378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.725151350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0881547
X-RAY DIFFRACTIONr_chiral_restr0.0850.21166
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216122
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 252 -
Rwork0.248 5229 -
obs--99.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4359-0.184-0.56790.12050.15690.3089-0.1303-0.18690.1856-0.01890.07960.09120.040.09910.05070.12540.0084-0.00690.13470.00390.2112-17.26-2.589-35.633
20.16-0.0092-0.17541.342-0.37770.35150.0289-0.02880.05920.0879-0.0549-0.1257-0.03810.07310.0260.1033-0.0166-0.01350.03220.02320.119924.7322.356-33.626
30.50920.25480.04990.80070.0961.14270.0126-0.04080.03050.1111-0.0557-0.0210.0744-0.04850.04320.0931-0.0052-0.01210.009-0.00020.030510.419-22.102-14.93
40.93180.5405-0.23871.0636-0.06850.3165-0.09120.31170.0508-0.1620.1420.03030.0095-0.1038-0.05080.1319-0.0322-0.01450.11050.02440.0169-3.658-6.542-60.26
50.8065-0.0157-0.07782.89980.41730.423-0.07090.1124-0.1850.1106-0.00590.00130.11170.03820.07680.10660.00520.03080.0327-0.0190.06019.409-26.435-47.331
60.72640.0478-0.44380.52150.04931.4525-0.0763-0.0204-0.2155-0.08110.0670.04640.04220.05290.00920.1236-0.04110.01050.0535-0.00390.0931-9.547-22.634-47.669
72.3638-0.10680.32820.45320.49821.9184-0.1078-0.4762-0.16990.02570.12880.0960.0068-0.1933-0.0210.08490.03780.0290.17080.080.0856-22.307-20.791-27.874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T3 - 18
2X-RAY DIFFRACTION1P103 - 115
3X-RAY DIFFRACTION1A1001
4X-RAY DIFFRACTION2A1 - 105
5X-RAY DIFFRACTION2A340 - 389
6X-RAY DIFFRACTION3A106 - 339
7X-RAY DIFFRACTION4A390 - 468
8X-RAY DIFFRACTION4A576 - 706
9X-RAY DIFFRACTION5A469 - 575
10X-RAY DIFFRACTION6A707 - 737
11X-RAY DIFFRACTION7A738 - 901

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